[gmx-users] protein topology

[Nikhil]

Thanks for your replay
here is the problem
my initial protein contain 8300 atoms with hydrogen,i deleted hydrogen 
then it comes around 4100 atoms,after pdb2gmx it become 5300 but doubt is 
what about remaining 3000 atoms? or hydrogens?
if i take with the 5300 atoms and follow the simulation it will be fine?
or is there anything im missing out here?
thanks
Nikhil